Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment,Journal of Hazardous Materials

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Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment
Journal of Hazardous Materials ( IF 12.2 ) Pub Date : 2024-02-14 , DOI: 10.1016/j.jhazmat.2024.133789
Tao Chen ₁ , Chunhao Mo ₁ , Yilin Yuan ₁ , Shengjie Li ₂ , Yinbao Wu ₁ , Xindi Liao ₁ , Yiwen Yang ₁

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Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms ( < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).

中文翻译：

短、长读长宏基因组和病毒组揭示了噬菌体介导的 ARGs 在猪废水处理的缺氧-含氧过程中的概况

噬菌体是传播最广泛的病毒之一，但它们的概况和它们在猪废水中携带的抗生素耐药基因（ARG）仍未得到充分探索。本研究使用短读长宏基因组和病毒组调查了噬菌体在养猪场缺氧/含氧（A/O）废水处理过程中的分布特征及其 ARG 风险。结果表明，病毒组可以提取比总宏基因组更多的噬菌体序列;因此，它更适合研究废水环境中的噬菌体。有趣的是，噬菌体的 ARG 丰度明显低于总微生物携带的 ARG （ < 0.01）。11 个 ARG 与噬菌体和细菌共存（R > 0.6 和 < 0.05），其中 Siphoviridae 是与大多数 ARG 共存的噬菌体（5）。在 Proteobacteria 和除 Bacteroidota 以外的主要门之间观察到水平基因转移（HGT）事件。此外，在细菌 MAGs 的同一重叠群上存在原噬菌体序列和 ARGs。这些数据有力地表明，在猪废水处理的 A/O 过程中，噬菌体促进 ARG 在细菌宿主之间的水平转移。因此，尽管噬菌体 ARG （pARG）的丰度较低，但不能忽视噬菌体介导的 ARG 水平转移的风险。

更新日期：2024-02-14

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